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I have read that table index compression happens just in MyISAM, but I came across
an article in dev.mysql that said: InnoDB supports table and index compression!
So now what is the pros of MyISAM?
Is there any reason left to use MyISAM? (except full-text search)

Is your question just about table index compression or in what cases would MyISAM be a better choice than InnoDB?
–
Craig EfreinDec 21 '11 at 8:16

"full-text search" and "spatial indexes" are probably the only things that should lead someone into using MyISAM engine.
–
ypercubeDec 21 '11 at 14:57

@CraigEfrein I wonder that we did not have any compression in InnoDB, but now this is another story. Maybe I am not very up to date :->
–
john.lockeDec 21 '11 at 16:17

I think that MyISAM is easier when it comes to maintenance and ease of use. I wrote up an answer to explain why, but I wasn't sure if that was what you were looking for.
–
Craig EfreinDec 21 '11 at 17:22

I appreciate your answer @CraigEfrein, Let me get this straight: do we have data compression in InnoDB?
–
john.lockeDec 21 '11 at 18:11

Recovering Disk Space

Once you do that, any InnoDB table that gets bloated can be shrunk. For example, if you have an InnoDB called mydb.mytable, you can shrink it with:

ALTER TABLE mydb.mytable ENGINE=InnoDB;

or

OPTIMIZE TABLE mydb.mytable;

Restoring Databases

@Craig is totally right on MyISAM.

As for InnoDB, restoring tables individually can be a nightmare. This is the case because tables are either inside ibdata1 (innodb_file_per_table=0) or outside (innodb_file_per_table=1).

For tables outside ibdata1, this is a 24/7 nightmare because the tablespace id of the .ibd file may change if a table is dropped and recreated throughout the course of a business day. If you backup the .ibd with its tablespace id that day, you cannot restore it to it DB Folder by dropping it in. You also cannot do any tricks ALTER TABLE tblname DISCARD TABLESPACE and ALTER TABLE tblname IMPORT TABLESPACE because the tablespace id is hardcoded. You have to write some custom adhoc scripts to pull off such a miracle in conjunction with ALTER TABLE tblname DISCARD TABLESPACE and ALTER TABLE tblname IMPORT TABLESPACE.

In MyISAM, you can delete a database on the File System without impacting the other databases and recover disk space. With InnoDB the ibdata file does not shrink when you remove databases. I have only been able to recover space in the ibdata file by deleting it and then restoring each remaining database. Perhaps someone knows a better way?

Restoring Databases

Another advantage to MyISAM is being able to restore a database using a backup system like bacula or Acronis. With MyISAM I can copy a database into and out of MySQL via file system commands, once again without affecting the other databases. With InnoDB, I have to do everything via the a MySQL client.

So I think that MyISAM is simpler to manage in certain situations. In a database that had a mixture of MyISAM and InnoDB, you would probably only be able to restore specific tables, but I haven't tried that yet.

As far as performance goes, a white paper from MySQL I recently read about 5.5 shows that InnoDB is better.